When the world's largest merchant ship ferries its monthly cargo of 13,000 containers between China and Europe it burns nearly 350 tonnes of fuel a day. The Emma Maersk supplies Britain with everything from toys and food to clothes and televisions, but its giant diesel engine can emit more than 300,000 tonnes of CO2 a year - equivalent to a medium-sized coal power station.

Until now reducing CO2 emissions from the world's fleet of almost 90,000 large ships has not been a priority for governments or shipowners. Previously, the accepted figure for shipping emissions - drawn from information supplied by the industry - has been a maximum of 400m tonnes of CO2, or around 1.8% of global emissions.

But with today's disclosure that emissions from shipping are three times higher than previously thought, many experts will be asking why the industry has escaped the attention of governments and environmental campaigners alike.

The world's burgeoning shipping fleet currently emits 1.21bn tonnes a year, the draft UN report seen by the Guardian says, constituting nearly 4.5% of world emissions.

Whereas the aviation industry has been at the top of the climate change agenda, and is expected to be included in the EU's trading scheme, emissions from ships, which emit twice as much CO2 as planes, have gone relatively unnoticed.

In Britain ship emissions are not covered in the climate change bill which commits Britain to cutting CO2 emissions by 60% by 2050, and there is no plan to control them, beyond suggestions by ministers that they should be included in the EU's emissions trading scheme, along with aviation. Shipping has also escaped the strict EU laws that govern emissions from cars and power stations.

Part of the problem, experts say, is that the industry has grown so rapidly - it now carries more than 90% of the world's trade by volume, and has tripled its tonnage carried since 1970 - and the shift of industrial production away from the US and Europe to China and south Asia has meant cargoes have to travel further.

The huge expansion of cargo ships, upon which import-reliant countries such as Britain have come to depend, has also taken place largely out of sight.

Making matters worse, ships have historically sailed between national jurisdictions; out on the high seas there is little regulation on what a ship can burn, and countries are unwilling to share responsibility.

The British government, for example, has always resisted counting the industry's emissions as part of the national total, because no international method has been agreed on how the gases emitted by ships should be allocated between countries.

Crucially, shipping exploits a ready supply of the world's cheapest, most polluting "bunker" fuel. Marine heavy fuel oil, which is burned by all large ships, is the residue of the world's oil refineries and is so thick that when cold it can be walked on. It is 60% cheaper than cleaner oils and, according to the report, demand for it is soaring.

"Bunker fuel is just waste oil, basically what is left over after all the cleaner fuels have been extracted from crude oil. It's tar, the same as asphalt. It's the cheapest and dirtiest fuel in the world," said Christian Eyde Moller, chief executive officer of the Rotterdam-based DK Group, a leading shipping technology company.

"The world's shipping fleet has grown very quickly. Ships are getting bigger and bigger, and they are burning more," he added.

"Their engines are now more efficient, which means they can burn thicker fuels, so they are emitting more pollution. The industry is more efficient per container than ever, but it has been ignoring fuel consumption and its corresponding impact on the environment and health."

The prognosis for an industry set to expand over the coming decade is not good. More than 3,000 ships, many of which are designed to carry similar-sized cargoes as the Emma Maersk, are expected to be built in the next three years, according to Lloyds Register of Shipping.

Together with the forecast expansion in world trade, the scientists estimate shipping emissions will grow 30% to 1.45bn tonnes within 12 years. This would make shipping responsible for nearly 6% of global emissions by 2020.

The UN report is expected to prompt a change in priorities among the climate change experts.

Already, the figures are a cause for anxieties at the Intergovernmental Panel on Climate Change (IPCC), the world's most trusted arbiter of the scale and impact of greenhouse gases.

Last year's IPCC reports into climate change relied on estimates for emissions from shipping which, it now seems, underestimated the damage ships are causing.

"This new figure significantly increases the challenge we face in terms of the likely impact [of climate change] we should expect and also the effort we should put in to mitigate and adapt," said Martin Parry, a co-chairman of the IPCC's climate change impacts working group II.

However the UN report does point to ways in which emissions from ships can be substantially cut. The simplest would be to make ships travel more slowly. One study has shown that if speeds were reduced by 10% it would lead to a 23% reduction of CO2 emissions. It also notes that shipowners could design more efficient ships, burn higher quality fuel, and fit vessels with "scrubbing" equipment to capture emissions on board.

Some inroads are already being made: although it is the world's largest ship of its kind, Emma Maersk is classed among the most energy efficient vessels afloat because it recycles its own heat.

But on the whole shipowners have resisted any controls, saying that if vessels were made to travel more slowly they would need to build more ships, which they argue would increase emissions.

At a glance

Percentage of global CO2 emissions produced by industrial emitters

Electricity 24%

Manufacturing 11%

Shipping 4.5%

Refineries 4%

Aviation 2%

Explainer: Health Implications

The International Maritime Organisation's assessment of the impact of shipping emissions has also discovered alarming levels of other air pollutants, some of which pose a serious risk to human health.

"Bunker fuel" - used by large ships - is rich in sulphur, the main component of acid rain and haze, as well as particulate matter: minute sooty specks directly linked to lung cancers, heart attacks and respiratory diseases.

The draft report says sulphur dioxide emissions from ships now stand at 16.2m tonnes a year and are expected by increase 40%, to 22.7m tonnes, by 2020. The forecast is in sharp contrast to land-based industries and vehicles, which have been forced by successive clean air laws to reduce emissions and use higher quality fuels.

Current EU rules limit the sulphur content of fuel in cars to 15 parts per million, against 45,000 parts per million for ships.

Emissions of nitrogen oxides and particulates are also shown to be far higher than previously thought. According to the report, ships release 25.8m tonnes of nitrogen oxides into the air, as well as 1.8m tonnes of tiny PM10 particles (particulate matter, less than 10 micrometres or less) which are linked to cancers and other diseases.

The shipping industry expects emissions - and pollutants - to increase by more than 30% in the next 12 years.

A peer-reviewed paper in the American Chemical Society's journal last month calculated that particulate matter pollution from the shipping industry currently causes 60,000 deaths a year, mostly along busy shipping routes. This could rise to 100,000 deaths within a few years if no action is taken to make ships burn cleaner fuel.